Purpose: The objective of this pilot study was to histologically evaluate bone regeneration using a self-assembling peptide hydrogel scaffold with recombinant human bone morphogenetic protein-2 (rhBMP-2) in a rabbit calvaria model. Materials and Methods: Five adult New Zealand White rabbits were used for the study. Each received four titanium cylinders, which were placed into perforated slits made in the outer cortical bone of the calvaria. The cylinders were filled with the following test materials: (1) unfilled control; (2) rhBMP-2; (3) PuraMatrix (PM), a synthetic self-assembling peptide (RADA16-I) consisting of a 16-amino acid sequence and with a three-dimensional structure; and (4) PM/rhBMP-2. Each cylinder was covered with a titanium lid. After 8 weeks, the animals were sacrificed, and ground sections were obtained for histomorphometric analysis. Results: Histomorphometric analysis showed that regenerated tissue in the cylinder with PM/rhBMP-2 was significantly increased compared to the empty control. The mean area values of regenerated tissue in the cylinders were 35.80% ± 10.35% (control), 47.94% ± 5.65% (rhBMP-2), 48.94% ± 11.33% (PM), and 58.06% ± 14.84% (PM/rhBMP-2). The mean area values of newly formed bone in the cylinders were 9.39% ± 4.34% (control), 14.03% ± 2.25% (rhBMP-2), 13.99% ± 2.15% (PM), and 16.61% ± 3.79% (PM/rhBMP-2). Neither rhBMP-2 nor PM alone significantly enhanced bone regeneration compared to the empty control cylinder. Conclusions: PM with rhBMP-2 significantly enhanced bone regeneration on the bone augmentation model in a rabbit. PM promises to be a useful alternative synthetic material as a carrier for rhBMP-2 for bone regeneration.